1. Minutes of the last meeting

2. Software Development

2.1 Graphics library

Alan has modified Jemboss. Cygwin no longer defines the SHELL
variable which is required by the Jemboss makefile. Even where it is
defined, cygwin now has ksh which is used by default and upsets ther make. users need to:

setenv CONFIG_SHELL /bin/tcsh
or
export CONFIG_SHELL=/bin/bash

Alan has successfully tested EMBOSS 4.0.0 with all patches on
an Intel Mac.

Peter has worked through the parsing of NCBI style IDs in FASTA
files. There were various issues including whether the database name
from the input file, the -sdbname option, or the -osdbname option
should be used in output. Also in some cases a database name could be
preserved from a previous entry - where NCBI format files had a
mixture of sequences with and without databases. New attributes were
required for sequence input and output objects to separate the command
line database name settings from those read in the input.

2.2 New applications

Peter has added a new application extractalign to
extract regions from a sequence alignment. It is a minor modification
of extractseq. Another application to appear soon is wordfinder
a modification of supermatcher to search for word-based near identical
hits in a (protein) database to help the pathogen sequencing group at
Sanger.

Peter investigated a request for a program that can handle
pattern matches with very large result sets. The user is happy with
the available programs. They ran slowly because he really does want an
enormous number of hits.

Peter has worked through past requests for applications and
features. He will collect them together so we can set priorities as a
"Dear Santa" list, with help from the user community.

2.3 Other development

Mahmut reported that LSF has been upgraded and SoapLab job
hangs have been fixed. Job submission is temporarily synchronous.

The database definition for EMBL has been changed to support historic
ID numbers. To fix the 2.8.0 server some applications were copied from
4.0.0. This appears to work.

Error messages for database access could be improved, especially for
SoapLab users who are guessing the USA syntax. It would be useful if
documentation URLs could be given in the SoapLab error messages.

Peter had discussions with the Taverna/OMII people in
Manchester about improving metadata support. SoapLab should report
pairs of mutually exclusive options (direct_data and usa sequence
input for example) as a version of the mandatory value. We also should
identify more carefully the minimum set of inputs needed for an
application to run so that these ports can be coloured and controlled
more easily in Taverna. The discussion also included ways to notify
Taverna that an application (or an entire soaplab server) is obsolete
and to point to an alternative server.

3. Administration

Alan reported that JEMBOSS has been patched to handle the new
pattern ACD type. There is a fix to the making of patch files to find
new files as well as changed files.

Peter is having meetings with local EMBOSS users to discuss
database configurations and application needs. The first meeting was
be with Babraham Research Institute last week. The ability to combine
databases would be useful as they have split EMBL into a number of
subdatabases. They are looking for an interface to suit their users
needs which include project management functions. Customizing wEMBOSS
was recommended as something worth investigating.

Alan is still working on obtaining purify.

4. Documentation and Training

Jon has completed conversion of the text from the ACD syntax
documentation, and the developers' course talks and
practicals. Placeholders are in the text. Master contents and XML
outlines will be completed next month.

Remaining work includes filling in a few gaps in the text, making the
style consistent, and checking the automatically generated
content. The nucleus library function names still need to be cleaned
up, although in most cases they are reasonably consistent already.

5. User queries and answers

The list was reviewed. Everyone should review the current list at
sf.net/projects/emboss/ and close those already dealt with. All
requests have been assigned (mostly to Peter).

All new issues were considered to be resolved.

6. AOB

7. Date Of Next Meeting

The next meeting is on
Monday 11th December. This will be the last meeting of 2006.